In my experience %TRANS (=TRANS/INPUT) has proved to be the most useful
measure but TRANS/TI can give you an idea about how important any
particular feature is in overall performance. TRANS itself is probably
less useful because the amount of information in each feature differs
considerably.

How you do the analyses depends on what questions you are trying to
answer. Analysing individual matrices and then doing standard
statistical tests is one way to avoid the difficulties of doing
statistical analyses on a small number of matrices (which require
something like log-linear analyses). On the other hand, looking at group
matrices can make it easier to spot trends.